Make native mvnd only require glibc 2.12 on ubuntu 22.04 (#825, fixes #823)

The modern glibc from 2.34 had two breaking changes: move all api in lib{pthread,dl,rt}.so into libc.so, new static start up code breaking the runtime compatibility for old glibc (<2.34). See https://developers.redhat.com/articles/2021/12/17/why-glibc-234-removed-libpthread for more info.

This commit has 3 changes to overcome these changes:
- override gcc path to redefine glibc symbols on the fly in the generated .o by graalvm when linking
- provide a dynamic startup code to support both old and modern runtime glibc
- add needed dynamic libraries: lib{pthread,rt,dl}.so.

.github/workflows/early-access.yaml

@@ -31,7 +31,7 @@ jobs:
   default-build:
     name: 'Default build (without Graal)'
     if: startsWith(github.event.head_commit.message, '[release] Release ') != true
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - name: 'Checkout'
         uses: actions/checkout@v3
@@ -52,7 +52,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-20.04, macOS-10.15, windows-2019 ]
+        os: [ ubuntu-22.04, macOS-10.15, windows-2019 ]
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -79,22 +79,38 @@ jobs:
         run: ./mvnw clean -Dmrm=false -B -ntp -e
 
       - name: 'Patch Graal libs for only requiring glibc 2.12'
+        if: ${{ env.OS == 'linux' }}
         shell: bash
         run: |
-          if [[ $OS == linux ]] && [[ $GRAALVM_HOME ]] && [[ -d "$GRAALVM_HOME/lib/static/linux-amd64/glibc" ]]; then
+          mkdir -p client/target/graalvm-libs-for-glibc-2.12
-            mkdir -p client/target/graalvm-libs-for-glibc-2.12
+
-            echo "memcpy memcpy@GLIBC_2.2.5" >client/target/glibc.redef
+          : patch common libraries
-            echo "posix_spawn posix_spawn@GLIBC_2.2.5" >>client/target/glibc.redef
+          ( find "$GRAALVM_HOME/lib/static/linux-amd64/glibc" -name '*.a'
-            find "$GRAALVM_HOME/lib/static/linux-amd64/glibc" -name '*.a' | while IFS= read -r input; do
+            ls -1 /lib/x86_64-linux-gnu/libz.a
-              output="client/target/graalvm-libs-for-glibc-2.12/$(basename -- "$input")"
+            ls -1 "$GRAALVM_HOME/lib/svm/clibraries/linux-amd64/libjvm.a"
-              objcopy --redefine-syms=client/target/glibc.redef -- "$input" "$output" 2>/dev/null
+            ls -1 "$GRAALVM_HOME/lib/svm/clibraries/linux-amd64/liblibchelper.a"
-            done
+          ) | while IFS= read -r input; do
-            find /usr/lib -name libz.a | xargs -r -I {} objcopy --redefine-syms=client/target/glibc.redef {} client/target/graalvm-libs-for-glibc-2.12/libz.a
+                output="client/target/graalvm-libs-for-glibc-2.12/$(basename -- "$input")"
-          fi
+                objcopy --redefine-syms=client/src/main/resources/glibc/glibc.redef -- "$input" "$output" 2>/dev/null
+              done
+
+          : patch gcc startfile
+          gcc -O3 -Wall -Wextra -Werror -Wconversion -Wsign-conversion -Wcast-qual -pedantic -c -o client/target/dynamic-libc-start.o client/src/main/resources/glibc/dynamic-libc-start.c
+          ld -r /lib/x86_64-linux-gnu/Scrt1.o client/target/dynamic-libc-start.o -o client/target/graalvm-libs-for-glibc-2.12/Scrt1.o
+          objcopy --redefine-syms=client/src/main/resources/glibc/glibc.redef client/target/graalvm-libs-for-glibc-2.12/Scrt1.o 2>/dev/null
 
       - name: 'Build native distribution'
         run: ./mvnw verify -Pnative -Dmrm=false -B -ntp -e
 
+      - name: 'Verify native binary for only requiring glibc 2.12'
+        if: ${{ env.OS == 'linux' }}
+        shell: bash
+        run: |
+          (( 4 == "$(ldd client/target/mvnd | awk '{print $1}' | sort -u | grep -c 'lib\(c\|dl\|rt\|pthread\)\.so\.[0-9]')" )) || ( ldd client/target/mvnd && false )
+          err=0
+          objdump -T client/target/mvnd | grep GLIBC_ | grep -v 'GLIBC_\([01]\|2\.[0-9]\|2\.1[012]\)[^0-9]' || err=$?
+          (( err == 1 ))
+
       - name: 'Upload daemon test logs'
         if: always()
         uses: actions/upload-artifact@v3

.github/workflows/release.yaml

@@ -35,7 +35,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: [ ubuntu-20.04, macOS-10.15, windows-2019 ]
+        os: [ ubuntu-22.04, macOS-10.15, windows-2019 ]
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -62,22 +62,38 @@ jobs:
         run: ./mvnw clean -Dmrm=false -B -ntp -e
 
       - name: 'Patch Graal libs for only requiring glibc 2.12'
+        if: ${{ env.OS == 'linux' }}
         shell: bash
         run: |
-          if [[ $OS == linux ]] && [[ $GRAALVM_HOME ]] && [[ -d "$GRAALVM_HOME/lib/static/linux-amd64/glibc" ]]; then
+          mkdir -p client/target/graalvm-libs-for-glibc-2.12
-            mkdir -p client/target/graalvm-libs-for-glibc-2.12
+
-            echo "memcpy memcpy@GLIBC_2.2.5" >client/target/glibc.redef
+          : patch common libraries
-            echo "posix_spawn posix_spawn@GLIBC_2.2.5" >>client/target/glibc.redef
+          ( find "$GRAALVM_HOME/lib/static/linux-amd64/glibc" -name '*.a'
-            find "$GRAALVM_HOME/lib/static/linux-amd64/glibc" -name '*.a' | while IFS= read -r input; do
+            ls -1 /lib/x86_64-linux-gnu/libz.a
-              output="client/target/graalvm-libs-for-glibc-2.12/$(basename -- "$input")"
+            ls -1 "$GRAALVM_HOME/lib/svm/clibraries/linux-amd64/libjvm.a"
-              objcopy --redefine-syms=client/target/glibc.redef -- "$input" "$output" 2>/dev/null
+            ls -1 "$GRAALVM_HOME/lib/svm/clibraries/linux-amd64/liblibchelper.a"
-            done
+          ) | while IFS= read -r input; do
-            find /usr/lib -name libz.a | xargs -r -I {} objcopy --redefine-syms=client/target/glibc.redef {} client/target/graalvm-libs-for-glibc-2.12/libz.a
+                output="client/target/graalvm-libs-for-glibc-2.12/$(basename -- "$input")"
-          fi
+                objcopy --redefine-syms=client/src/main/resources/glibc/glibc.redef -- "$input" "$output" 2>/dev/null
+              done
+
+          : patch gcc startfile
+          gcc -O3 -Wall -Wextra -Werror -Wconversion -Wsign-conversion -Wcast-qual -pedantic -c -o client/target/dynamic-libc-start.o client/src/main/resources/glibc/dynamic-libc-start.c
+          ld -r /lib/x86_64-linux-gnu/Scrt1.o client/target/dynamic-libc-start.o -o client/target/graalvm-libs-for-glibc-2.12/Scrt1.o
+          objcopy --redefine-syms=client/src/main/resources/glibc/glibc.redef client/target/graalvm-libs-for-glibc-2.12/Scrt1.o 2>/dev/null
 
       - name: 'Build native distribution'
         run: ./mvnw verify -Pnative -Dmrm=false -B -ntp -e -DskipTests -s .mvn/release-settings.xml
 
+      - name: 'Verify native binary for only requiring glibc 2.12'
+        if: ${{ env.OS == 'linux' }}
+        shell: bash
+        run: |
+          (( 4 == "$(ldd client/target/mvnd | awk '{print $1}' | sort -u | grep -c 'lib\(c\|dl\|rt\|pthread\)\.so\.[0-9]')" )) || ( ldd client/target/mvnd && false )
+          err=0
+          objdump -T client/target/mvnd | grep GLIBC_ | grep -v 'GLIBC_\([01]\|2\.[0-9]\|2\.1[012]\)[^0-9]' || err=$?
+          (( err == 1 ))
+
       - name: 'Upload artifact'
         uses: actions/upload-artifact@v3
         with:
@@ -90,7 +106,7 @@ jobs:
 
   source:
     name: 'Build source distributions'
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - name: 'Check out repository'
         uses: actions/checkout@v3
@@ -123,7 +139,7 @@ jobs:
             target/maven-mvnd-*.tar.gz
 
   release:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     needs: [build, source]
 
     steps:

client/pom.xml

@@ -34,6 +34,7 @@
     <maven.compiler.release>11</maven.compiler.release>
     <graalvm-native-static-opt />
     <graalvm-native-glibc-opt />
+    <patchelf.skip>true</patchelf.skip>
   </properties>
 
   <dependencies>
@@ -199,7 +200,10 @@
         </file>
       </activation>
       <properties>
-        <graalvm-native-glibc-opt>-H:CLibraryPath=${project.build.directory}/graalvm-libs-for-glibc-2.12</graalvm-native-glibc-opt>
+        <graalvm-native-glibc-opt>-H:CCompilerPath=${basedir}/src/main/resources/glibc/gcc
+                                  -H:CCompilerOption=-B${project.build.directory}/graalvm-libs-for-glibc-2.12
+                                  -H:CLibraryPath=${project.build.directory}/graalvm-libs-for-glibc-2.12</graalvm-native-glibc-opt>
+        <patchelf.skip>false</patchelf.skip>
       </properties>
     </profile>
 
@@ -235,6 +239,32 @@
               </execution>
             </executions>
           </plugin>
+          <plugin>
+            <groupId>org.codehaus.mojo</groupId>
+            <artifactId>exec-maven-plugin</artifactId>
+            <configuration>
+              <skip>${patchelf.skip}</skip>
+              <executable>patchelf</executable>
+              <arguments>
+                <argument>--add-needed</argument>
+                <argument>libpthread.so.0</argument>
+                <argument>--add-needed</argument>
+                <argument>librt.so.1</argument>
+                <argument>--add-needed</argument>
+                <argument>libdl.so.2</argument>
+                <argument>${project.build.directory}/mvnd</argument>
+              </arguments>
+            </configuration>
+            <executions>
+              <execution>
+                <id>add-needed-glibc-so</id>
+                <goals>
+                  <goal>exec</goal>
+                </goals>
+                <phase>package</phase>
+              </execution>
+            </executions>
+          </plugin>
         </plugins>
       </build>
     </profile>

client/src/main/resources/glibc/dynamic-libc-start.c

@@ -0,0 +1,67 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+/* ref:
+ *   https://elixir.bootlin.com/glibc/glibc-2.37.9000/source/csu/libc-start.c
+ *   https://elixir.bootlin.com/glibc/glibc-2.33.9000/source/csu/elf-init.c#L68
+ */
+
+#define _GNU_SOURCE
+#include <dlfcn.h>
+#include <stdint.h>
+
+__asm__(".symver dlsym,dlsym@GLIBC_2.2.5");
+__asm__(".symver dlvsym,dlvsym@GLIBC_2.2.5");
+
+/* These magic symbols are provided by the linker.  */
+extern void (*__init_array_start[])(int, char **, char **) __attribute__ ((visibility ("hidden")));
+extern void (*__init_array_end[])(int, char **, char **) __attribute__ ((visibility ("hidden")));
+extern void _init(void);
+
+/* These functions are passed to __libc_start_main by the startup code.
+   These get statically linked into each program. */
+
+static void
+__libc_csu_init(const int argc, char **const argv, char **const envp)
+{
+  _init();
+  const __auto_type size = __init_array_end - __init_array_start;
+  for (__auto_type i = 0; i < size; ++i)
+    (*__init_array_start[i])(argc, argv, envp);
+}
+
+int
+__dynamic_libc_start_main(int (*const main)(int, char **, char **),
+                          const int argc,
+                          char ** const argv,
+                          __typeof(&__libc_csu_init) init,
+                          void (*const fini)(void),
+                          void (*const rtld_fini)(void),
+                          void (*const stack_end))
+{
+  _Static_assert(sizeof(uintptr_t) >= sizeof(void*), "uintptr_t should contain a object pointer");
+  _Static_assert(sizeof(uintptr_t) <= sizeof(&__dynamic_libc_start_main), "function pointer should contain an uintptr_t");
+
+  const __auto_type __libc_start_main = (__typeof(&__dynamic_libc_start_main))(uintptr_t)dlsym(RTLD_DEFAULT, "__libc_start_main");
+  if (!dlvsym(RTLD_DEFAULT, "__libc_start_main", "GLIBC_2.34")) {
+    init = &__libc_csu_init; // old runtime glibc, ver < 2.34
+  }
+
+  return __libc_start_main(main, argc, argv, init, fini, rtld_fini, stack_end);
+}

client/src/main/resources/glibc/gcc

@@ -0,0 +1,27 @@
+#!/bin/sh
+
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+set -euf
+
+base=$(dirname -- "$0")
+
+# fix glibc api version on the fly
+find . -name '*.o' -print0 | xargs -0rn 1 objcopy --redefine-syms="$base/glibc.redef"
+
+exec gcc "$@"

client/src/main/resources/glibc/glibc.redef

@@ -0,0 +1,35 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+__libc_start_main __dynamic_libc_start_main
+clock_gettime clock_gettime@GLIBC_2.2.5
+dlopen dlopen@GLIBC_2.2.5
+dlsym dlsym@GLIBC_2.2.5
+memcpy memcpy@GLIBC_2.2.5
+posix_spawn posix_spawn@GLIBC_2.2.5
+pthread_attr_getguardsize pthread_attr_getguardsize@GLIBC_2.2.5
+pthread_attr_getstack pthread_attr_getstack@GLIBC_2.2.5
+pthread_attr_setstacksize pthread_attr_setstacksize@GLIBC_2.2.5
+pthread_condattr_setclock pthread_condattr_setclock@GLIBC_2.3.3
+pthread_create pthread_create@GLIBC_2.2.5
+pthread_getattr_np pthread_getattr_np@GLIBC_2.2.5
+pthread_join pthread_join@GLIBC_2.2.5
+pthread_kill pthread_kill@GLIBC_2.2.5
+pthread_setname_np pthread_setname_np@GLIBC_2.12
+sem_destroy sem_destroy@GLIBC_2.2.5
+sem_init sem_init@GLIBC_2.2.5
+sem_post sem_post@GLIBC_2.2.5
+sem_wait sem_wait@GLIBC_2.2.5

native/pom.xml

@@ -71,7 +71,6 @@
       <plugin>
         <groupId>org.codehaus.mojo</groupId>
         <artifactId>exec-maven-plugin</artifactId>
-        <version>3.0.0</version>
         <dependencies>
           <dependency>
             <groupId>info.picocli</groupId>

pom.xml

@@ -485,6 +485,11 @@
           <artifactId>maven-wrapper-plugin</artifactId>
           <version>3.1.1</version>
         </plugin>
+        <plugin>
+          <groupId>org.codehaus.mojo</groupId>
+          <artifactId>exec-maven-plugin</artifactId>
+          <version>3.1.0</version>
+        </plugin>
       </plugins>
     </pluginManagement>